Pacific Biosciences Releases Software Upgrade to Support Full-Length Transcript Sequencing

MENLO PARK, Calif., March 31, 2014 (GLOBE NEWSWIRE) — Pacific Biosciences of California, Inc., (Nasdaq:PACB) provider of the PacBio® RS II, today announced the release of a software upgrade for its Single Molecule, Real-Time (SMRT®) DNA Sequencing platform. SMRT Analysis 2.2 provides enhanced functionality to support two additional applications that uniquely benefit from the company’s long-read sequencing technology: Iso-Seq™ full-length transcript/isoform sequencing, and human leukocyte antigen (HLA) haplotype phasing.

The study of mRNA transcript isoforms has been challenging due to the short read lengths of other sequencing technologies. Long PacBio reads enable full-length transcript sequencing, as well as the identification of alternatively spliced forms of a gene. As a result, new genes and isoforms are accessible for study.

For example, Steve Quake and Thomas Südhof, Professors at Stanford University and Investigators with the Howard Hughes Medical Institute, together with colleagues, used SMRT Sequencing to characterize the genes encoding neurexins, which are involved in the formation of connections between cells in the human braini. Because of the high number of different splice isoforms, these genes have been extremely difficult to study and, despite extensive efforts, the full extent of neurexin alternative splicing remained unclear. Using PacBio long-read sequencing, the researchers identified hundreds of different isoforms in the neurexin gene family, highlighting a staggering complexity of these gene products and providing more insight to the notion that neurexins function as recognition molecules that contribute to the specification of cell connections in the brain. 

The Iso-Seq application can also be used for transcriptome-wide studies, improving the ability to annotate genes in reference genomes.  Long sequence reads spanning full-length gene transcripts will eliminate the need for an RNA-seq assembly step, providing more complete gene models and more comprehensive annotation of transcribed genes.

Michael Snyder’s lab at Stanford University demonstrated the utility of PacBio long-read sequencing for assessing transcribed regions across the human genome in a paperii last October.  Dr. Snyder commented: “Full length transcriptome sequencing allows the analysis of complete transcriptomes including the deciphering of complex transcripts and the discovering of new ones. PacBio sequencing works remarkably well for this.”

The second new application is HLA haplotype phasing. The HLA loci are a group of genes critical to immune system function. In humans, the HLA genes are extraordinarily polymorphic. Several thousand alleles have been described and the number of new alleles continues to increase. HLA allele-specific genotyping is critical for autoimmune disease-association studies, drug hypersensitivity research and other applications. Accurate phasing of HLA polymorphisms has previously required several experiments at great expense. The long reads provided by PacBio sequencing are ideally suited for accurate allele-level genotyping with unambiguous allele phasing.

PacBio’s SMRT Analysis 2.2 generates consensus sequences that can be input into third-party software for HLA analysis. This data has successfully been used with the Conexio Genomics (Perth, Australia) Assign MPS sequence analysis software.

“PacBio’s analysis pipeline independently generates the consensus sequence of each allele in a heterozygous sample, including non-coding regions,” said David Sayer, Chief Executive Officer of Conexio Genomics. “When analyzed in our sequence analysis software, this data results in a completely phased, immutable HLA genotype. The analysis is simple and rapid.”

“The SMRT Analysis 2.2 upgrade streamlines two important applications that are uniquely enabled by our robust long-read sequencing technology,” said Michael Hunkapiller, President and CEO of Pacific Biosciences. “We are excited about the trajectory that has unfolded with each increase in the performance of the PacBio RS II system, and look forward to seeing what novel insights the research community will uncover with these new applications.”

The new SMRT Analysis software upgrade is available for download from Pacific Biosciences’ DevNet website. To access the software, data, and documentation, visit

For more information on the new SMRT Analysis software and the PacBio RS II, please visit

About the PacBio RS II and SMRT Sequencing

Pacific Biosciences’ Single Molecule, Real-Time (SMRT) Sequencing technology achieves the industry’s longest read lengths, highest consensus accuracyiii,iv and the least degree of bias.v These characteristics, combined with the ability to detect many types of DNA base modifications (e.g., methylation) as part of the sequencing process, make the PacBio RS II an essential tool for many scientists for studying genetic and genomic variation. The PacBio platform is being used as the sequencing solution to address a growing number of complex medical, agricultural and industrial problems.

About Pacific Biosciences

Pacific Biosciences of California, Inc. (Nasdaq:PACB) offers the PacBio RS II DNA Sequencing System to help scientists solve genetically complex problems. Based on its novel Single Molecule, Real-Time (SMRT) technology, the company’s products enable: targeted sequencing to more comprehensively characterize genetic variations; de novo genome assembly to more fully identify, annotate and decipher genomic structures; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. By providing access to information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.

i Treutlein et al., “Cartography of neurexin alternative splicing mapped by single-molecule long-read mRNA sequencing.” PNAS, 10.1073/pnas.1403244111 (2014).

ii Sharon et al., “A single-molecule long-read survey of the human transcriptome,” Nature Biotechnology 31, 1009–1014 (2013).

iii Koren et al., “Reducing assembly complexity of microbial genomes with single-molecule sequencing.” Genome Biology, 14:R10.1 (2013).

iv Chin et al., “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.” Nature Methods, 10; 563-569 (2013).

v Ross et al. Characterizing and measuring bias in sequence data. Genome Biol 14: R51 (2013).

For Pacific Biosciences:

Nicole Litchfield
For Pacific Biosciences

Trevin Rard
Pacific Biosciences

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